VARIATIONS OF AMINO ACID SEQUENCES OF THE NUCLEOCAPSID PROTEIN FROM COVID-19 PATIENTS IN JAVA, INDONESIA

• Main Author: Dibya Iranisha, Chalissa
• Format: Final Project
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/62635
• Institution: Institut Teknologi Bandung

SARS-CoV-2 is a new type of coronavirus that attacks the human respiratory system and is the cause of COVID-19 disease. SARS-CoV-2 has spread rapidly throughout the world with a very high mutation rate resulting in various variants. Studies regarding the impact of the SARS-CoV-2 variants and their relationship to vaccine development are still being studied until now. One of the main structural proteins of SARS-CoV-2 that has begun to be studied is the nucleocapsid (N) protein. Nucleocapsid protein is a RNA-binding protein that plays important roles in many aspects of the viral life cycle, including the regulation of the immune system. The important role of the multifunctional nucleocapsid protein is considered to be able to make it a candidate for antiviral drugs. Therefore, this study aimed to identify the variations of amino acid sequences of the SARS-CoV-2 nucleocapsid protein and the lineage of the mutated variants. Sample data of COVID-19 patients in Java, Indonesia were collected from the GISAID database, then aligned with the MAFFT alignment program. Variations of amino acid sequences and their phylogenetic relationships were analyzed using MEGA X software. The results of phylogenetic analysis showed that 10 groups of the lineage of SARS-CoV-2 variants from the identification of a total of 227 mutational variations in nucleocapsid protein regions scattered across Java, Indonesia have evolved rapidly from Wuhan-Hu-1. The structural model prediction analysis which was then carried out using an artificial intelligence-based system, AlphaFold 2 produced structures that were quite similar to the experimental structures. However, the deletion at residues 314-419 greatly affects the function of the N-CTD domain that makes up the SARS-CoV-2 nucleocapsid protein.